Updating with new info:
Synchronization doesn't wipe styles on elements as long as there is no element on the page styled with 'basic paragraph' paragraph style. Once there is, everything is reset after synchronization.
What exact version of InDesign?
What exact version of your OS?
I was having this same problem. I'm on CS6 and updated an existing book with 12 different files. First, I updated some aspects of the styles (Paragraph, Character and Object) in the master document and grouped them for organization's sake. Then when I synchronized, all of the text defaulted to Body Copy, even my headings. So I went back to the master doc and ungrouped them, saved, resynchronized, reapplied styles and saved that doc. To see if it was still happening, I synchronized again. Problem repeated: everything that wasn't locked on the master was reset to my Body Copy style.
Then I got to thinking... I went back to my default text box object style in the master doc and changed the paragraph style to a header that automatically applies the next style. As suspected, when I resynched, all of my text in the unlocked boxes switched to that NEW style. There was nothing wrong with my TEXT styles, but with my OBJECT styles. Check your text box defaults and make sure "Paragraph Styles" is unchecked.